In high-risk cardiac operating rooms (ORs), the cognitive alignment of surgical teams is critical for performance and patient safety. This study investigates the cognitive processes in cardiac surgery teams, focusing on potential misalignments among surgeons, anesthesiologists, and perfusionists during coronary artery bypass grafting (CABG) procedures. Through Cognitive Task Analysis of 9 expert participants, we examined decision-making, communication, and problem-solving strategies across CABG phases. We quantified cognitive process misalignments, revealing 137 unique intraoperative cognitive processes with significant variations in perceived cognitive workload across different surgical steps. Misalignment analysis identified specific phases with notable discrepancies, such as “clamp aorta and deliver cardioplegia” and “anastomoses,” where the misalignment scores were 12 and 10, respectively, between surgeons and anesthesiologists. A Spearman correlation analysis also yielded a coefficient of 0.42 (p < 0.01), indicating a positive correlation between team-level perceived cognitive load and misalignment. These results highlight the need for targeted interventions to improve team coordination and cognitive alignment in cardiac surgery, potentially enhancing patient care and efficiency. This study also provides a preliminary data-driven framework for understanding team dynamics in high-pressure medical environments and informs the development of training programs to foster cognitive alignment in surgical teams.